Serum metaviromic profiling of yaks and Tibetan sheep provides a pre-harvest viral baseline for food-producing ruminants.

Pre-harvest viral profiles of food-producing ruminants in high-altitude pastoral systems remain poorly defined, limiting the selection of viral targets for monitoring along animal-derived food chains. In this study, we performed viral metagenomic profiling of 142 pooled serum libraries generated from 712 individual blood samples collected from yaks and Tibetan sheep across the Qinghai-Tibet Plateau. A total of 2.87 billion raw reads were obtained, of which 26.34 million were assigned to viral taxa. The serum viromes were dominated by single-stranded DNA and single-stranded RNA viruses, with Parvoviridae being the most abundant family. Yaks harboured significantly greater viral richness and diversity than Tibetan sheep, and community-level analysis showed distinct host-associated virome structures. Phylogenetic reconstruction recovered parvovirus-, astrovirus-, hepacivirus-, and genomovirus-related sequences, including a divergent erythroparvovirus-related lineage; the nepovirus-related sequence was categorized separately as a likely dietary or environmentally derived viral nucleic acid signal. These findings provide a serum-based viral reference for high-altitude pastoral production systems and identify viral lineages that may be considered for exploratory screening in downstream matrices, pending validation of their presence and infectivity. While viral nucleic acids detected in serum do not directly indicate contamination of animal-derived foods or foodborne transmission, they provide baseline data on serum-associated viral diversity that can guide subsequent assessment of potential spillover and food-chain relevance.